LAMMPS (27 Nov 2018)
  using 1 OpenMP thread(s) per MPI task
# fix gcmc example with fix shake

# variables available on command line

variable        mu index -8.1
variable	disp index 0.5
variable        temp index 338.0
variable        lbox index 10.0
variable        spacing index 5.0

# global model settings

units           real
atom_style      full
boundary        p p p
pair_style      lj/cut/coul/long  14
pair_modify     mix arithmetic tail yes
kspace_style    ewald 0.0001
bond_style      harmonic
angle_style     harmonic

# box, start molecules on simple cubic lattice

lattice 	sc ${spacing}
lattice 	sc 5.0
Lattice spacing in x,y,z = 5 5 5
region          box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
region          box block 0 10.0 0 ${lbox} 0 ${lbox} units box
region          box block 0 10.0 0 10.0 0 ${lbox} units box
region          box block 0 10.0 0 10.0 0 10.0 units box
create_box      2 box                                       bond/types 1                                angle/types 1                               extra/bond/per/atom 2                       extra/angle/per/atom 1                      extra/special/per/atom 2
Created orthogonal box = (0 0 0) to (10 10 10)
  1 by 1 by 1 MPI processor grid

molecule        h2omol H2O.txt
Read molecule h2omol:
  3 atoms with max type 2
  2 bonds with max type 1
  1 angles with max type 1
  0 dihedrals with max type 0
  0 impropers with max type 0
create_atoms   	0 box mol h2omol 464563 units box
Created 24 atoms
  Time spent = 0.00128841 secs

# rigid SPC/E water model

pair_coeff      1 1 0.15535 3.166
pair_coeff      * 2 0.0000 0.0000

bond_coeff      1     1000       1.0
angle_coeff     1      100       109.47

# masses

mass 1 15.9994
mass 2 1.0

# MD settings

group           h2o type 1 2
24 atoms in group h2o
neighbor        2.0 bin
neigh_modify    every 1 delay 1 check yes
velocity       	all create ${temp} 54654
velocity       	all create 338.0 54654
timestep        1.0

minimize 0.0 0.0 100 1000
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Ewald initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.170448
  estimated absolute RMS force accuracy = 0.0332064
  estimated relative force accuracy = 0.0001
  KSpace vectors: actual max1d max3d = 16 2 62
                  kxmax kymax kzmax  = 2 2 2
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 16
  ghost atom cutoff = 16
  binsize = 8, bins = 2 2 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d/newton
      bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.88 | 11.88 | 11.88 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0          338   -4.1890564 9.2628112e-06     18.98377    739.06991 
     100          338   -36.122455   0.67828405   -12.271354    573.22675 
Loop time of 0.0461962 on 1 procs for 100 steps with 24 atoms

98.3% CPU use with 1 MPI tasks x 1 OpenMP threads

Minimization stats:
  Stopping criterion = max iterations
  Energy initial, next-to-last, final = 
        -4.18904713252      -34.586018764     -35.4441713339
  Force two-norm initial, final = 18.0027 42.115
  Force max component initial, final = 5.8993 15.4907
  Final line search alpha, max atom move = 0.00127226 0.0197082
  Iterations, force evaluations = 100 239

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.038526   | 0.038526   | 0.038526   |   0.0 | 83.40
Bond    | 0.00031209 | 0.00031209 | 0.00031209 |   0.0 |  0.68
Kspace  | 0.0019636  | 0.0019636  | 0.0019636  |   0.0 |  4.25
Neigh   | 0.00055456 | 0.00055456 | 0.00055456 |   0.0 |  1.20
Comm    | 0.0040288  | 0.0040288  | 0.0040288  |   0.0 |  8.72
Output  | 1.5259e-05 | 1.5259e-05 | 1.5259e-05 |   0.0 |  0.03
Modify  | 0          | 0          | 0          |   0.0 |  0.00
Other   |            | 0.0007958  |            |       |  1.72

Nlocal:    24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    2011 ave 2011 max 2011 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    4921 ave 4921 max 4921 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 4921
Ave neighs/atom = 205.042
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
reset_timestep 0

# rigid constraints with thermostat

fix             mynvt h2o nvt temp ${temp} ${temp} 100
fix             mynvt h2o nvt temp 338.0 ${temp} 100
fix             mynvt h2o nvt temp 338.0 338.0 100
fix             wshake h2o shake 0.0001 50 0 b 1 a 1 mol h2omol
  0 = # of size 2 clusters
  0 = # of size 3 clusters
  0 = # of size 4 clusters
  8 = # of frozen angles

# important to make temperature dofs dynamic

compute_modify  thermo_temp dynamic/dof yes
compute_modify  mynvt_temp dynamic/dof yes

run 1000
Ewald initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.170448
  estimated absolute RMS force accuracy = 0.0332064
  estimated relative force accuracy = 0.0001
  KSpace vectors: actual max1d max3d = 16 2 62
                  kxmax kymax kzmax  = 2 2 2
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    518.26667   -36.122455            0   -12.949638    703.43827 
    1000    260.39219   -55.141232            0   -43.498537    -1698.672 
Loop time of 0.140376 on 1 procs for 1000 steps with 24 atoms

Performance: 615.489 ns/day, 0.039 hours/ns, 7123.720 timesteps/s
99.1% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 0.10434    | 0.10434    | 0.10434    |   0.0 | 74.33
Bond    | 0.00013041 | 0.00013041 | 0.00013041 |   0.0 |  0.09
Kspace  | 0.008199   | 0.008199   | 0.008199   |   0.0 |  5.84
Neigh   | 0.0061581  | 0.0061581  | 0.0061581  |   0.0 |  4.39
Comm    | 0.015352   | 0.015352   | 0.015352   |   0.0 | 10.94
Output  | 1.4305e-05 | 1.4305e-05 | 1.4305e-05 |   0.0 |  0.01
Modify  | 0.004544   | 0.004544   | 0.004544   |   0.0 |  3.24
Other   |            | 0.001639   |            |       |  1.17

Nlocal:    24 ave 24 max 24 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    1776 ave 1776 max 1776 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    5073 ave 5073 max 5073 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 5073
Ave neighs/atom = 211.375
Ave special neighs/atom = 2
Neighbor list builds = 27
Dangerous builds = 0
reset_timestep 0

# gcmc

variable        tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
fix             mygcmc h2o gcmc 100 100 0 0 54341 ${temp} ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 ${mu} ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 ${disp} mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert ${tfac} group h2o shake wshake
fix             mygcmc h2o gcmc 100 100 0 0 54341 338.0 -8.1 0.5 mol                 h2omol tfac_insert 1.66666666666667 group h2o shake wshake

# atom counts

variable 	oxygen atom "type==1"
variable 	hydrogen atom "type==2"
group 	        oxygen dynamic all var oxygen
dynamic group oxygen defined
group 		hydrogen dynamic all var hydrogen
dynamic group hydrogen defined
variable        nO equal count(oxygen)
variable        nH equal count(hydrogen)

# output

variable	tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
variable	iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
variable	dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
variable	racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
thermo_style    custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH
thermo          1000

# run

run             20000
Ewald initialization ...
  using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
  G vector (1/distance) = 0.170448
  estimated absolute RMS force accuracy = 0.0332064
  estimated relative force accuracy = 0.0001
  KSpace vectors: actual max1d max3d = 16 2 62
                  kxmax kymax kzmax  = 2 2 2
WARNING: Fix gcmc using full_energy option (src/MC/fix_gcmc.cpp:487)
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:471)
Per MPI rank memory allocation (min/avg/max) = 11.63 | 11.63 | 11.63 Mbytes
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc v_nO v_nH 
       0    260.39219   -1699.3643   -55.141232    11.642695   0.23910963       24            0            0            0            0            8           16 
    1000    340.44409   -2560.1501   -280.70157    53.784356   0.80699501       81  0.054205983  0.015933081            0            0           27           54 
    2000    302.57602    592.41718   -310.37771    53.213377   0.89666113       90  0.030546787 0.0078577743            0            0           30           60 
    3000    270.18045   -817.18659   -346.75773    50.737466   0.95643854       96  0.021969243 0.0060076096            0            0           32           64 
    4000    334.17192    1153.3017   -335.25519     62.75449   0.95643854       96  0.016400775 0.0045269353            0            0           32           64 
    5000    360.36872   -647.99689    -336.2928    67.674015   0.95643854       96  0.012996731 0.0036569014            0            0           32           64 
    6000    282.37822   -986.51765   -341.91848    53.028098   0.95643854       96  0.010941282 0.0030159847            0            0           32           64 
    7000    363.01448    2952.0391   -358.72963    70.335018   0.98632724       99 0.0098923151 0.0028884203            0            0           33           66 
    8000    331.70391    323.34886   -382.04165    68.223498    1.0461046      105 0.0092083323 0.0025112378            0            0           35           70 
    9000     337.2032   -3637.5257   -390.66472     69.35457    1.0461046      105 0.0081585853 0.0022395915            0            0           35           70 
   10000    373.67063    3081.3271    -380.5107    76.855041    1.0461046      105 0.0073396679 0.0020164949            0            0           35           70 
   11000    336.64665    5535.9451   -405.21548    71.247059    1.0759934      108 0.0068442571 0.0018355023            0            0           36           72 
   12000    306.51164    1448.1757    -410.3655    64.869362    1.0759934      108 0.0062798499 0.0016809265            0            0           36           72 
   13000    319.03497    177.44405   -406.17113    67.519768    1.0759934      108 0.0057952448 0.0015520479            0            0           36           72 
   14000    309.89701   -1022.6798   -384.20239    65.585833    1.0759934      108  0.005391524 0.0014384143            0            0           36           72 
   15000    398.91559    2058.9251   -404.32604    84.425503    1.0759934      108 0.0050257238 0.0013442486            0            0           36           72 
   16000    318.98778    873.46142   -392.13338     67.50978    1.0759934      108 0.0047204383 0.0012578458            0            0           36           72 
   17000    333.16025    2347.0215   -387.73943    70.509206    1.0759934      108 0.0044407568 0.0011843991            0            0           36           72 
   18000    353.23789    -2305.787    -382.1633    74.758389    1.0759934      108 0.0042016342 0.0011165574            0            0           36           72 
   19000    322.70939    5619.9631   -381.81328    68.297412    1.0759934      108 0.0039877848 0.0010558436            0            0           36           72 
   20000    371.07261    3916.1113   -389.76357    78.532884    1.0759934      108 0.0037874635 0.0010033009            0            0           36           72 
Loop time of 242.59 on 1 procs for 20000 steps with 108 atoms

Performance: 7.123 ns/day, 3.369 hours/ns, 82.444 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 38.279     | 38.279     | 38.279     |   0.0 | 15.78
Bond    | 0.055672   | 0.055672   | 0.055672   |   0.0 |  0.02
Kspace  | 0.60623    | 0.60623    | 0.60623    |   0.0 |  0.25
Neigh   | 4.4189     | 4.4189     | 4.4189     |   0.0 |  1.82
Comm    | 1.2719     | 1.2719     | 1.2719     |   0.0 |  0.52
Output  | 0.00096583 | 0.00096583 | 0.00096583 |   0.0 |  0.00
Modify  | 197.85     | 197.85     | 197.85     |   0.0 | 81.56
Other   |            | 0.1098     |            |       |  0.05

Nlocal:    108 ave 108 max 108 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    8000 ave 8000 max 8000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    100006 ave 100006 max 100006 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 100006
Ave neighs/atom = 925.981
Ave special neighs/atom = 2
Neighbor list builds = 20903
Dangerous builds = 0

Total wall time: 0:04:02
